McGillis married fellow Juilliard student Boyd Black in 1979, but the couple divorced in 1981.[21]

In February 1982, McGillis and her live-in girlfriend were assaulted, verbally abused, and raped at knifepoint by two men who broke into their New York apartment. This experience encouraged the actress to pursue her film role as the lawyer who supports Jodie Foster's character in The Accused.[22]

McGillis married Fred Tillman in 1989, and they have two daughters. The couple divorced in 2002.[23]

McGillis came out as a lesbian in April 2009 during an interview with SheWired.[24][25] McGillis said that coming to terms with her sexual orientation has been an ongoing process since age 12, and she was long convinced that God was punishing her for being homosexual with the aforementioned rape incident.[24][25] In 2010, McGillis entered into a civil union with Melanie Leis, a Philadelphia-based sales executive; she and McGillis met in 2000 when Leis was a bartender at the "Kellys' Caribbean Bar Grill & Brewery" in Key West, Florida, which McGillis owned with her then-husband Fred Tillman.[26] Leis and McGillis broke up in 2011.

McGillis was reportedly assaulted by a stranger who broke into her North Carolina home on June 17, 2016.[29] She said the attack, as well as others she has experienced in the past, has led her to decide to apply for a concealed carry gun permit to protect herself.[30]

^Mottram, James (February 21, 2014). "Kelly McGillis: 'I would cameo in Top Gun 2'". The Independent. Retrieved July 12, 2016. McGillis moved to New York in 1979 to study acting at the prestigious Julliard [sic] drama school, the same year she married fellow student Boyd Black. It was short-lived, the couple divorcing in 1981